| 4987 |
10.1016/j.ajog.2018.10.018 |
Does The Human Placenta Delivered At Term Have A
Microbiota? Results Of Cultivation, Quantitative Real-Time Pcr, 16S Rrna
Gene Sequencing, And Metagenomics |
Theis, Kevin R.; Romero, Roberto, 0000-0002-4448-5121;
Winters, Andrew D.; Greenberg, Jonathan M.; Gomez-Lopez, Nardhy;
Alhousseini, Ali; Bieda, Janine; Maymon, Eli; Pacora, Percy; Fettweis,
Jennifer M.; Buck, Gregory A.; Jefferson, Kimberly K.,
0000-0003-1052-1988; Strauss, Jerome F.; Erez, Offer,
0000-0002-0680-7652; Hassan, Sonia S. |
American Journal Of Obstetrics And Gynecology |
2019 |
| 7069 |
10.1016/j.cej.2018.09.218 |
Removal Of Antibiotic Resistance Genes And Control Of
Horizontal Transfer Risk By Uv, Chlorination And Uv/Chlorination
Treatments Of Drinking Water |
Zhang, Tianyang, 0000-0002-9522-5354; Hu, Yaru; Jiang,
Lei; Yao, Shijie; Lin, Kuangfei; Zhou, Yanbo, 0000-0003-1756-7073; Cui,
Changzheng |
Chemical Engineering Journal |
2019 |
| 7539 |
10.1016/j.cell.2018.10.029 |
Us Immigration Westernizes The Human Gut
Microbiome |
Vangay, Pajau; Johnson, Abigail J.; Ward, Tonya L.;
Al-Ghalith, Gabriel A.; Shields-Cutler, Robin R.; Hillmann, Benjamin M.;
Lucas, Sarah K.; Beura, Lalit K.; Thompson, Emily A.; Till, Lisa M.;
Batres, Rodolfo; Paw, Bwei; Pergament, Shannon L.; Saenyakul,
Pimpanitta; Xiong, Mary; Kim, Austin D.; Kim, Grant; Masopust, David;
Martens, Eric C.; Angkurawaranon, Chaisiri; Mcgready, Rose; Kashyap,
Purna C.; Culhane-Pera, Kathleen A.; Knights, Dan |
Cell |
2018 |
| 7585 |
10.1016/j.cell.2019.01.001 |
Extensive Unexplored Human Microbiome Diversity
Revealed By Over 150,000 Genomes From Metagenomes Spanning Age,
Geography, And Lifestyle |
Pasolli, Edoardo; Asnicar, Francesco; Manara, Serena;
Zolfo, Moreno; Karcher, Nicolai; Armanini, Federica; Beghini, Francesco;
Manghi, Paolo; Tett, Adrian; Ghensi, Paolo; Collado, Maria Carmen; Rice,
Benjamin L.; Dulong, Casey; Morgan, Xochitl C.; Golden, Christopher D.;
Quince, Christopher; Huttenhower, Curtis; Segata, Nicola,
0000-0002-1583-5794 |
Cell |
2019 |
| 7704 |
10.1016/j.cell.2019.07.010 |
Benchmarking Metagenomics Tools For Taxonomic
Classification |
Ye, Simon H.; Siddle, Katherine J.; Park, Daniel J.;
Sabeti, Pardis C. |
Cell |
2019 |
| 8416 |
10.1016/j.chom.2018.06.005 |
Mother-To-Infant Microbial Transmission From Different
Body Sites Shapes The Developing Infant Gut Microbiome |
Ferretti, Pamela; Pasolli, Edoardo; Tett, Adrian;
Asnicar, Francesco; Gorfer, Valentina; Fedi, Sabina; Armanini, Federica;
Truong, Duy Tin; Manara, Serena; Zolfo, Moreno; Beghini, Francesco;
Bertorelli, Roberto; De Sanctis, Veronica; Bariletti, Ilaria; Canto,
Rosarita; Clementi, Rosanna; Cologna, Marina; Crifo, Tiziana; Cusumano,
Giuseppina; Gottardi, Stefania; Innamorati, Claudia; Mase, Caterina;
Postai, Daniela; Savoi, Daniela; Duranti, Sabrina; Lugli, Gabriele
Andrea; Mancabelli, Leonardo; Turroni, Francesca; Ferrario, Chiara;
Milani, Christian; Mangifesta, Marta; Anzalone, Rosaria; Viappiani,
Alice; Yassour, Moran; Vlamakis, Hera; Xavier, Ramnik; Collado, Carmen
Maria; Koren, Omry; Tateo, Saverio; Soffiati, Massimo; Pedrotti, Anna;
Ventura, Marco; Huttenhower, Curtis; Bork, Peer; Segata, Nicola,
0000-0002-1583-5794 |
Cell Host & Microbe |
2018 |
| 8428 |
10.1016/j.chom.2019.01.004 |
Distinct Genetic And Functional Traits Of Human
Intestinal Prevotella Copri Strains Are Associated With Different
Habitual Diets |
De Filippis, Francesca; Pasolli, Edoardo; Tett, Adrian;
Tarallo, Sonia; Naccarati, Alessio; De Angelis, Maria; Neviani, Erasmo;
Cocolin, Luca; Gobbetti, Marco; Segata, Nicola; Ercolini, Danilo |
Cell Host & Microbe |
2019 |
| 8432 |
10.1016/j.chom.2019.01.011 |
Composition And Variation Of The Human Milk Microbiota
Are Influenced By Maternal And Early-Life Factors |
Moossavi, Shirin, 0000-0002-8329-9970; Sepehri, Shadi;
Robertson, Bianca; Bode, Lars; Goruk, Sue; Field, Catherine J.; Lix,
Lisa M.; De Souza, Russell J.; Becker, Allan B.; Mandhane, Piushkumar
J.; Turvey, Stuart E.; Subbarao, Padmaja; Moraes, Theo J.; Lefebvre,
Diana L.; Sears, Malcolm R.; Khafipour, Ehsan; Azad, Meghan B. |
Cell Host & Microbe |
2019 |
| 8438 |
10.1016/j.chom.2019.03.007 |
Adaptive Evolution Within Gut Microbiomes Of Healthy
People |
Zhao, Shijie; Lieberman, Tami D.; Poyet, Mathilde;
Kauffman, Kathryn M.; Gibbons, Sean M.; Groussin, Mathieu; Xavier,
Ramnik J.; Alm, Eric J. |
Cell Host & Microbe |
2019 |
| 8447 |
10.1016/j.chom.2019.08.018 |
The Prevotella Copri Complex Comprises Four Distinct
Clades Underrepresented In Westernized Populations |
Tett, Adrian; Huang, Kun D.; Asnicar, Francesco;
Fehlner-Peach, Hannah; Pasolli, Edoardo; Karcher, Nicolai; Armanini,
Federica; Manghi, Paolo; Bonham, Kevin; Zolfo, Moreno; De Filippis,
Francesca; Magnabosco, Cara; Bonneau, Richard; Lusingu, John; Amuasi,
John; Reinhard, Karl; Rattei, Thomas; Boulund, Fredrik; Engstrand, Lars;
Zink, Albert; Collado, Maria Carmen; Littman, Dan R.; Eibach, Daniel;
Ercolini, Danilo; Rota-Stabelli, Omar; Huttenhower, Curtis; Maixner,
Frank; Segata, Nicola |
Cell Host & Microbe |
2019 |
| 10146 |
10.1016/j.envint.2018.03.044 |
Antibiotic Resistance In Wastewater Treatment Plants:
Tackling The Black Box |
Manaia, Celia M., 0000-0002-3674-1789; Rocha,
Jaqueline; Scaccia, Nazareno, 0000-0003-3294-3815; Marano, Roberto,
0000-0001-7805-6360; Radu, Elena; Biancullo, Francesco,
0000-0002-4363-9141; Cerqueira, Francisco, 0000-0003-4812-0880;
Fortunato, Gianuario; Iakovides, Iakovos C.; Zammit, Ian,
0000-0002-9768-6592; Kampouris, Ioannis; Vaz-Moreira, Ivone,
0000-0001-8912-9836; Nunes, Olga C., 0000-0003-4742-2537 |
Environment International |
2018 |
| 10149 |
10.1016/j.envint.2018.04.041 |
Critical Knowledge Gaps And Research Needs Related To
The Environmental Dimensions Of Antibiotic Resistance |
Larsson, D.G. Joakim; Andremont, Antoine;
Bengtsson-Palme, Johan, 0000-0002-6528-3158; Brandt, Kristian Koefoed,
0000-0001-7886-9708; De Roda Husman, Ana Maria; Fagerstedt, Patriq,
0000-0002-6639-3412; Fick, Jerker, 0000-0002-3949-7371; Flach,
Carl-Fredrik; Gaze, William H.; Kuroda, Makoto, 0000-0002-0487-4405;
Kvint, Kristian; Laxminarayan, Ramanan, 0000-0002-1390-9016; Manaia,
Celia M., 0000-0002-3674-1789; Nielsen, Kaare Magne; Plant, Laura; Ploy,
Marie-Cecile; Segovia, Carlos; Simonet, Pascal; Smalla, Kornelia; Snape,
Jason; Topp, Edward; Van Hengel, Arjon J.; Verner-Jeffreys, David W.;
Virta, Marko P.J.; Wellington, Elizabeth M.; Wernersson, Ann-Sofie |
Environment International |
2018 |
| 10177 |
10.1016/j.envint.2019.01.034 |
Understanding Drivers Of Antibiotic Resistance Genes In
High Arctic Soil Ecosystems |
Mccann, Clare M.; Christgen, Beate,
0000-0002-5662-8847; Roberts, Jennifer A.; Su, Jian-Qiang; Arnold,
Kathryn E.; Gray, Neil D.; Zhu, Yong-Guan; Graham, David W. |
Environment International |
2019 |
| 10201 |
10.1016/j.envint.2019.05.036 |
Metagenomic And Metatranscriptomic Analyses Reveal
Activity And Hosts Of Antibiotic Resistance Genes In Activated
Sludge |
Liu, Zongbao; Klumper, Uli; Liu, Yang; Yang, Yuchun;
Wei, Qiaoyan; Lin, Jih-Gaw; Gu, Ji-Dong; Li, Meng |
Environment International |
2019 |
| 10205 |
10.1016/j.envint.2019.104912 |
Transfer Of Antibiotic Resistance From Manure-Amended
Soils To Vegetable Microbiomes |
Zhang, Yu-Jing; Hu, Hang-Wei; Chen, Qing-Lin; Singh,
Brajesh K.; Yan, Hui; Chen, Deli; He, Ji-Zheng |
Environment International |
2019 |
| 10329 |
10.1016/j.envpol.2019.112996 |
A Review On Removing Antibiotics And Antibiotic
Resistance Genes From Wastewater By Constructed Wetlands: Performance
And Microbial Response |
Liu, Xiaohui; Guo, Xiaochun; Liu, Ying; Lu, Shaoyong;
Xi, Beidou; Zhang, Jian; Wang, Zhi; Bi, Bin |
Environmental Pollution |
2019 |
| 13076 |
10.1016/j.jenvman.2019.05.090 |
Insights On The Current Status Of Occurrence And
Removal Of Antibiotics In Wastewater By Advanced Oxidation
Processes |
Anjali, R.; Shanthakumar, S. |
Journal Of Environmental Management |
2019 |
| 16847 |
10.1016/j.scitotenv.2019.03.162 |
Antibiotic Resistance In Drinking Water Systems:
Occurrence, Removal, And Human Health Risks |
Sanganyado, Edmond, 0000-0001-6244-3059; Gwenzi,
Willis, 0000-0003-3149-1052 |
Science Of The Total Environment |
2019 |
| 16885 |
10.1016/j.scitotenv.2019.05.315 |
Antibiotic Microbial Resistance (Amr) Removal
Efficiencies By Conventional And Advanced Wastewater Treatment
Processes: A Review |
Hiller, C.X.; Hubner, U.; Fajnorova, S.; Schwartz, T.;
Drewes, J.E., 0000-0003-2520-7596 |
Science Of The Total Environment |
2019 |
| 16914 |
10.1016/j.scitotenv.2019.134023 |
Antibiotic Resistance Genes Identified In Wastewater
Treatment Plant Systems <U+2013> A Review |
Pazda, Magdalena; Kumirska, Jolanta,
0000-0003-1211-1114; Stepnowski, Piotr; Mulkiewicz, Ewa,
0000-0001-6144-1190 |
Science Of The Total Environment |
2019 |
| 17308 |
10.1016/j.soilbio.2018.08.018 |
Antibiotic Resistance Genes And Associated Bacterial
Communities In Agricultural Soils Amended With Different Sources Of
Animal Manures |
Han, Xue-Mei; Hu, Hang-Wei; Chen, Qing-Lin; Yang,
Li-Yuan; Li, He-Lian; Zhu, Yong-Guan; Li, Xiang-Zhen; Ma, Yi-Bing |
Soil Biology And Biochemistry |
2018 |
| 17707 |
10.1016/j.tim.2018.06.007 |
Evolution Of Plasmid-Mediated Antibiotic Resistance In
The Clinical Context |
San Millan, Alvaro |
Trends In Microbiology |
2018 |
| 17709 |
10.1016/j.tim.2018.09.008 |
The Human Microbiome And Child Growth <U+2013>
First 1000 Days And Beyond |
Robertson, Ruairi C., 0000-0002-3719-2056; Manges, Amee
R.; Finlay, B. Brett; Prendergast, Andrew J. |
Trends In Microbiology |
2019 |
| 17710 |
10.1016/j.tim.2018.11.003 |
Contamination In Low Microbial Biomass Microbiome
Studies: Issues And Recommendations |
Eisenhofer, Raphael, 0000-0002-3843-0749; Minich,
Jeremiah J.; Marotz, Clarisse; Cooper, Alan; Knight, Rob; Weyrich, Laura
S. |
Trends In Microbiology |
2019 |
| 17715 |
10.1016/j.tim.2019.08.001 |
The Gut Microbiota In The First Decade Of Life |
Derrien, Muriel; Alvarez, Anne-Sophie; De Vos, Willem
M. |
Trends In Microbiology |
2019 |
| 17826 |
10.1016/j.tplants.2019.02.010 |
Antibiotic Resistomes In Plant Microbiomes |
Chen, Qing-Lin; Cui, Hui-Ling; Su, Jian-Qiang;
Penuelas, Josep; Zhu, Yong-Guan |
Trends In Plant Science |
2019 |
| 18144 |
10.1016/j.watres.2018.08.048 |
Comparison Of The Uv/Chlorine And Uv/H2O2 Processes In
The Degradation Of Ppcps In Simulated Drinking Water And Wastewater:
Kinetics, Radical Mechanism And Energy Requirements |
Guo, Kaiheng, 0000-0002-8168-4605; Wu, Zihao; Yan,
Shuwen; Yao, Bo; Song, Weihua, 0000-0001-7633-7919; Hua, Zhechao; Zhang,
Xuewen; Kong, Xiujuan; Li, Xuchun; Fang, Jingyun |
Water Research |
2018 |
| 18158 |
10.1016/j.watres.2018.11.041 |
Ppcp Degradation And Dbp Formation In The Solar/Free
Chlorine System: Effects Of Ph And Dissolved Oxygen |
Hua, Zhechao; Guo, Kaiheng, 0000-0002-8168-4605; Kong,
Xiujuan; Lin, Suiki; Wu, Zihao; Wang, Liping; Huang, Huang; Fang,
Jingyun |
Water Research |
2019 |
| 18206 |
10.1016/j.watres.2019.06.039 |
Antibiotic Resistance Genes In Treated Wastewater And
In The Receiving Water Bodies: A Pan-European Survey Of Urban
Settings |
Cacace, Damiano, 0000-0003-1725-1044; Fatta-Kassinos,
Despo; Manaia, Celia M., 0000-0002-3674-1789; Cytryn, Eddie,
0000-0001-7805-6360; Kreuzinger, Norbert; Rizzo, Luigi,
0000-0003-1449-9116; Karaolia, Popi; Schwartz, Thomas; Alexander,
Johannes; Merlin, Christophe; Garelick, Hemda; Schmitt, Heike; De Vries,
Daisy; Schwermer, Carsten U.; Meric, Sureyya; Ozkal, Can Burak,
0000-0001-9576-2582; Pons, Marie-Noelle; Kneis, David; Berendonk, Thomas
U. |
Water Research |
2019 |
| 20176 |
10.1021/acs.est.8b04393 |
Degradation And Deactivation Of Bacterial Antibiotic
Resistance Genes During Exposure To Free Chlorine, Monochloramine,
Chlorine Dioxide, Ozone, Ultraviolet Light, And Hydroxyl Radical |
He, Huan; Zhou, Peiran; Shimabuku, Kyle K.,
0000-0001-8497-5945; Fang, Xuzhi; Li, Shu; Lee, Yunho,
0000-0001-5923-4897; Dodd, Michael C., 0000-0001-7544-1642 |
Environmental Science & Technology |
2019 |
| 20229 |
10.1021/acs.est.9b02462 |
Rate Constants And Mechanisms Of The Reactions Of
Cl<U+2022> And Cl2<U+2022><U+2013> With Trace Organic
Contaminants |
Lei, Yu; Cheng, Shuangshuang; Luo, Na; Yang, Xin,
0000-0001-9860-423X; An, Taicheng, 0000-0001-6918-8070 |
Environmental Science & Technology |
2019 |
| 22106 |
10.1038/nbt.4229 |
A Standardized Bacterial Taxonomy Based On Genome
Phylogeny Substantially Revises The Tree Of Life |
Parks, Donovan H; Chuvochina, Maria; Waite, David W;
Rinke, Christian, 0000-0003-4632-1187; Skarshewski, Adam; Chaumeil,
Pierre-Alain; Hugenholtz, Philip, 0000-0001-5386-7925 |
Nature Biotechnology |
2018 |
| 22307 |
10.1038/s41396-018-0277-8 |
Wastewater Treatment Plant Resistomes Are Shaped By
Bacterial Composition, Genetic Exchange, And Upregulated Expression In
The Effluent Microbiomes |
Ju, Feng, 0000-0003-4137-5928; Beck, Karin; Yin,
Xiaole; Maccagnan, Andreas; Mcardell, Christa S., 0000-0002-5251-7541;
Singer, Heinz P., 0000-0002-8542-3699; Johnson, David R.,
0000-0002-6728-8462; Zhang, Tong; Burgmann, Helmut,
0000-0002-5651-5906 |
The Isme Journal |
2018 |
| 22318 |
10.1038/s41396-019-0446-4 |
Linking The Resistome And Plasmidome To The
Microbiome |
Stalder, Thibault; Press, Maximilian O.; Sullivan,
Shawn; Liachko, Ivan; Top, Eva M., 0000-0002-6380-8782 |
The Isme Journal |
2019 |
| 22324 |
10.1038/s41396-019-0553-2 |
Breast Milk-Derived Human Milk Oligosaccharides Promote
Bifidobacterium Interactions Within A Single Ecosystem |
Lawson, Melissa A. E.; O’Neill, Ian J.; Kujawska,
Magdalena, 0000-0002-8842-3512; Gowrinadh Javvadi, Sree; Wijeyesekera,
Anisha, 0000-0001-6151-5065; Flegg, Zak; Chalklen, Lisa,
0000-0002-6162-9940; Hall, Lindsay J., 0000-0001-8938-5709 |
The Isme Journal |
2019 |
| 22327 |
10.1038/s41396-020-0590-x |
Anaerobic Methane Oxidation Coupled To Manganese
Reduction By Members Of The Methanoperedenaceae |
Leu, Andy O.; Cai, Chen, 0000-0002-0167-1397; Mcilroy,
Simon J., 0000-0003-3749-8730; Southam, Gordon; Orphan, Victoria J.;
Yuan, Zhiguo, 0000-0002-7566-1482; Hu, Shihu; Tyson, Gene W.,
0000-0001-8559-9427 |
The Isme Journal |
2020 |
| 22610 |
10.1038/s41467-018-06393-w |
Maternal Gut And Breast Milk Microbiota Affect Infant
Gut Antibiotic Resistome And Mobile Genetic Elements |
Parnanen, Katariina; Karkman, Antti; Hultman, Jenni,
0000-0002-3431-1785; Lyra, Christina; Bengtsson-Palme, Johan,
0000-0002-6528-3158; Larsson, D. G. Joakim, 0000-0002-5496-0328;
Rautava, Samuli; Isolauri, Erika; Salminen, Seppo; Kumar, Himanshu;
Satokari, Reetta; Virta, Marko, 0000-0001-5981-7566 |
Nature Communications |
2018 |
| 22614 |
10.1038/s41467-018-06473-x |
Meta-Analysis Of Effects Of Exclusive Breastfeeding On
Infant Gut Microbiota Across Populations |
Ho, Nhan T.; Li, Fan; Lee-Sarwar, Kathleen A.; Tun,
Hein M.; Brown, Bryan P.; Pannaraj, Pia S.; Bender, Jeffrey M.; Azad,
Meghan B.; Thompson, Amanda L.; Weiss, Scott T.; Azcarate-Peril, M.
Andrea; Litonjua, Augusto A.; Kozyrskyj, Anita L.; Jaspan, Heather B.;
Aldrovandi, Grace M.; Kuhn, Louise |
Nature Communications |
2018 |
| 22687 |
10.1038/s41467-018-07418-0 |
Expansive Microbial Metabolic Versatility And
Biodiversity In Dynamic Guaymas Basin Hydrothermal Sediments |
Dombrowski, Nina, 0000-0003-1917-2577; Teske, Andreas
P.; Baker, Brett J. |
Nature Communications |
2018 |
| 22714 |
10.1038/s41467-018-07631-x |
Birth Mode Is Associated With Earliest Strain-Conferred
Gut Microbiome Functions And Immunostimulatory Potential |
Wampach, Linda; Heintz-Buschart, Anna,
0000-0002-9780-1933; Fritz, Joelle V.; Ramiro-Garcia, Javier; Habier,
Janine; Herold, Malte; Narayanasamy, Shaman; Kaysen, Anne; Hogan, Angela
H.; Bindl, Lutz, 0000-0003-1764-434X; Bottu, Jean; Halder, Rashi,
0000-0002-1402-1254; Sjoqvist, Conny; May, Patrick, 0000-0001-8698-3770;
Andersson, Anders F., 0000-0002-3627-6899; De Beaufort, Carine; Wilmes,
Paul |
Nature Communications |
2018 |
| 22717 |
10.1038/s41467-018-07641-9 |
High Throughput Ani Analysis Of 90K Prokaryotic Genomes
Reveals Clear Species Boundaries |
Jain, Chirag; Rodriguez-R, Luis M.,
0000-0001-7603-3093; Phillippy, Adam M.; Konstantinidis, Konstantinos
T.; Aluru, Srinivas |
Nature Communications |
2018 |
| 22771 |
10.1038/s41467-018-07992-3 |
Fecal Pollution Can Explain Antibiotic Resistance Gene
Abundances In Anthropogenically Impacted Environments |
Karkman, Antti, 0000-0003-0983-3319; Parnanen,
Katariina; Larsson, D. G. Joakim, 0000-0002-5496-0328 |
Nature Communications |
2019 |
| 22899 |
10.1038/s41467-019-08844-4 |
Microbial Abundance, Activity And Population Genomic
Profiling With Motus2 |
Milanese, Alessio, 0000-0002-7050-2239; Mende, Daniel
R, 0000-0001-6831-4557; Paoli, Lucas; Salazar, Guillem; Ruscheweyh,
Hans-Joachim; Cuenca, Miguelangel, 0000-0003-3435-9102; Hingamp, Pascal;
Alves, Renato, 0000-0002-7212-0234; Costea, Paul I, 0000-0003-1645-3947;
Coelho, Luis Pedro, 0000-0002-9280-7885; Schmidt, Thomas S. B.,
0000-0001-8587-4177; Almeida, Alexandre, 0000-0001-8803-0893; Mitchell,
Alex L; Finn, Robert D., 0000-0001-8626-2148; Huerta-Cepas, Jaime; Bork,
Peer, 0000-0002-2627-833X; Zeller, Georg, 0000-0003-1429-7485; Sunagawa,
Shinichi, 0000-0003-3065-0314 |
Nature Communications |
2019 |
| 22900 |
10.1038/s41467-019-08853-3 |
Global Monitoring Of Antimicrobial Resistance Based On
Metagenomics Analyses Of Urban Sewage |
Hendriksen, Rene S.; Munk, Patrick,
0000-0001-8813-4019; Njage, Patrick; Van Bunnik, Bram,
0000-0003-2177-7073; Mcnally, Luke; Lukjancenko, Oksana; Roder, Timo;
Nieuwenhuijse, David; Pedersen, Susanne Karlsmose; Kjeldgaard, Jette;
Kaas, Rolf S.; Clausen, Philip Thomas Lanken Conradsen; Vogt, Josef
Korbinian; Leekitcharoenphon, Pimlapas; Van De Schans, Milou G. M.;
Zuidema, Tina; De Roda Husman, Ana Maria; Rasmussen, Simon,
0000-0001-6323-9041; Petersen, Bent; Amid, Clara; Cochrane, Guy;
Sicheritz-Ponten, Thomas; Schmitt, Heike; Alvarez, Jorge Raul Matheu;
Aidara-Kane, Awa; Pamp, Sunje J.; Lund, Ole; Hald, Tine; Woolhouse,
Mark; Koopmans, Marion P.; Vigre, Hakan; Petersen, Thomas Nordahl;
Aarestrup, Frank M., 0000-0002-7116-2723 |
Nature Communications |
2019 |
| 22967 |
10.1038/s41467-019-09252-4 |
Perinatal Factors Affect The Gut Microbiota Up To Four
Years After Birth |
Fouhy, Fiona, 0000-0002-8285-7694; Watkins, Claire;
Hill, Cian J.; O’Shea, Carol-Anne; Nagle, Brid; Dempsey, Eugene M.;
O’Toole, Paul W.; Ross, R. Paul; Ryan, C. Anthony; Stanton,
Catherine |
Nature Communications |
2019 |
| 22987 |
10.1038/s41467-019-09364-x |
Asgard Archaea Capable Of Anaerobic Hydrocarbon
Cycling |
Seitz, Kiley W.; Dombrowski, Nina, 0000-0003-1917-2577;
Eme, Laura, 0000-0002-0510-8868; Spang, Anja; Lombard, Jonathan; Sieber,
Jessica R.; Teske, Andreas P.; Ettema, Thijs J. G., 0000-0002-6898-6377;
Baker, Brett J. |
Nature Communications |
2019 |
| 23141 |
10.1038/s41467-019-10656-5 |
Establishing Microbial Composition Measurement
Standards With Reference Frames |
Morton, James T.; Marotz, Clarisse,
0000-0002-1520-8854; Washburne, Alex; Silverman, Justin; Zaramela, Livia
S., 0000-0002-1065-3799; Edlund, Anna; Zengler, Karsten,
0000-0002-8062-3296; Knight, Rob, 0000-0002-0975-9019 |
Nature Communications |
2019 |
| 23358 |
10.1038/s41467-019-13443-4 |
Phylogenomics Of 10,575 Genomes Reveals Evolutionary
Proximity Between Domains Bacteria And Archaea |
Zhu, Qiyun, 0000-0002-3568-6271; Mai, Uyen; Pfeiffer,
Wayne; Janssen, Stefan, 0000-0003-0955-0589; Asnicar, Francesco,
0000-0003-3732-1468; Sanders, Jon G., 0000-0001-6077-4014; Belda-Ferre,
Pedro, 0000-0001-6532-1161; Al-Ghalith, Gabriel A., 0000-0002-6953-6319;
Kopylova, Evguenia; Mcdonald, Daniel; Kosciolek, Tomasz,
0000-0002-9915-7387; Yin, John B.; Huang, Shi; Salam, Nimaichand; Jiao,
Jian-Yu; Wu, Zijun; Xu, Zhenjiang Z.; Cantrell, Kalen; Yang, Yimeng,
0000-0003-4819-1005; Sayyari, Erfan; Rabiee, Maryam; Morton, James T.;
Podell, Sheila, 0000-0001-7073-5190; Knights, Dan; Li, Wen-Jun,
0000-0002-1233-736X; Huttenhower, Curtis, 0000-0002-1110-0096; Segata,
Nicola, 0000-0002-1583-5794; Smarr, Larry; Mirarab, Siavash,
0000-0001-5410-1518; Knight, Rob, 0000-0002-0975-9019 |
Nature Communications |
2019 |
| 23497 |
10.1038/s41467-020-16366-7 |
Precise Phylogenetic Analysis Of Microbial Isolates And
Genomes From Metagenomes Using Phylophlan 3.0 |
Asnicar, Francesco, 0000-0003-3732-1468; Thomas, Andrew
Maltez, 0000-0001-5789-3354; Beghini, Francesco, 0000-0002-8105-9607;
Mengoni, Claudia; Manara, Serena, 0000-0001-6371-528X; Manghi, Paolo;
Zhu, Qiyun; Bolzan, Mattia, 0000-0001-8539-9468; Cumbo, Fabio,
0000-0003-2920-5838; May, Uyen; Sanders, Jon G., 0000-0001-6077-4014;
Zolfo, Moreno, 0000-0001-6661-4046; Kopylova, Evguenia; Pasolli,
Edoardo; Knight, Rob, 0000-0002-0975-9019; Mirarab, Siavash,
0000-0001-5410-1518; Huttenhower, Curtis, 0000-0002-1110-0096; Segata,
Nicola, 0000-0002-1583-5794 |
Nature Communications |
2020 |
| 23951 |
10.1038/s41559-019-1040-x |
Phylogenomics Provides Robust Support For A Two-Domains
Tree Of Life |
Williams, Tom A., 0000-0003-1072-0223; Cox, Cymon J.,
0000-0002-4927-979X; Foster, Peter G.; Szoll<U+0151>si, Gergely
J.; Embley, T. Martin |
Nature Ecology & Evolution |
2019 |
| 24332 |
10.1038/s41564-018-0171-1 |
Recovery Of Genomes From Metagenomes Via A
Dereplication, Aggregation And Scoring Strategy |
Sieber, Christian M. K.; Probst, Alexander J.; Sharrar,
Allison; Thomas, Brian C.; Hess, Matthias; Tringe, Susannah G.,
0000-0001-6479-8427; Banfield, Jillian F., 0000-0001-8203-8771 |
Nature Microbiology |
2018 |
| 24335 |
10.1038/s41564-018-0202-y |
Recognizing The Reagent Microbiome |
De Goffau, Marcus C.; Lager, Susanne; Salter, Susannah
J.; Wagner, Josef; Kronbichler, Andreas; Charnock-Jones, D. Stephen;
Peacock, Sharon J.; Smith, Gordon C. S.; Parkhill, Julian |
Nature Microbiology |
2018 |
| 24344 |
10.1038/s41564-018-0321-5 |
Genomic Variation And Strain-Specific Functional
Adaptation In The Human Gut Microbiome During Early Life |
Vatanen, Tommi, 0000-0003-0949-1291; Plichta, Damian
R.; Somani, Juhi; Munch, Philipp C.; Arthur, Timothy D.; Hall, Andrew
Brantley; Rudolf, Sabine; Oakeley, Edward J.; Ke, Xiaobo; Young, Rachel
A.; Haiser, Henry J.; Kolde, Raivo; Yassour, Moran; Luopajarvi,
Kristiina; Siljander, Heli; Virtanen, Suvi M.; Ilonen, Jorma; Uibo,
Raivo; Tillmann, Vallo; Mokurov, Sergei; Dorshakova, Natalya; Porter,
Jeffrey A.; Mchardy, Alice C., 0000-0003-2370-3430; Lahdesmaki, Harri;
Vlamakis, Hera; Huttenhower, Curtis, 0000-0002-1110-0096; Knip, Mikael,
0000-0003-0474-0033; Xavier, Ramnik J., 0000-0002-5630-5167 |
Nature Microbiology |
2018 |
| 24355 |
10.1038/s41564-019-0363-3 |
Wide Diversity Of Methane And Short-Chain Alkane
Metabolisms In Uncultured Archaea |
Borrel, Guillaume, 0000-0003-4893-8180; Adam,
Panagiotis S.; Mckay, Luke J., 0000-0003-2942-1821; Chen, Lin-Xing;
Sierra-Garcia, Isabel Natalia; Sieber, Christian M. K.; Letourneur,
Quentin; Ghozlane, Amine; Andersen, Gary L.; Li, Wen-Jun,
0000-0002-1233-736X; Hallam, Steven J., 0000-0002-4889-6876; Muyzer,
Gerard, 0000-0002-2422-0732; De Oliveira, Valeria Maia; Inskeep, William
P., 0000-0002-5203-817X; Banfield, Jillian F., 0000-0001-8203-8771;
Gribaldo, Simonetta, 0000-0002-7662-021X |
Nature Microbiology |
2019 |
| 24360 |
10.1038/s41564-019-0406-9 |
Proposal Of The Reverse Flow Model For The Origin Of
The Eukaryotic Cell Based On Comparative Analyses Of Asgard Archaeal
Metabolism |
Spang, Anja, 0000-0002-6518-8556; Stairs, Courtney W.,
0000-0001-6650-0970; Dombrowski, Nina; Eme, Laura, 0000-0002-0510-8868;
Lombard, Jonathan; Caceres, Eva F.; Greening, Chris,
0000-0001-7616-0594; Baker, Brett J.; Ettema, Thijs J. G.,
0000-0002-6898-6377 |
Nature Microbiology |
2019 |
| 24362 |
10.1038/s41564-019-0409-6 |
Transmission Of Human-Associated Microbiota Along
Family And Social Networks |
Brito, Ilana L.; Gurry, Thomas; Zhao, Shijie; Huang,
Katherine; Young, Sarah K.; Shea, Terrence P.; Naisilisili, Waisea;
Jenkins, Aaron P.; Jupiter, Stacy D.; Gevers, Dirk; Alm, Eric J.,
0000-0001-8294-9364 |
Nature Microbiology |
2019 |
| 24364 |
10.1038/s41564-019-0426-5 |
Global Diversity And Biogeography Of Bacterial
Communities In Wastewater Treatment Plants |
Wu, Linwei; Ning, Daliang; Zhang, Bing; Li, Yong;
Zhang, Ping; Shan, Xiaoyu; Zhang, Qiuting; Brown, Mathew Robert; Li,
Zhenxin; Van Nostrand, Joy D., 0000-0001-9548-6450; Ling, Fangqiong;
Xiao, Naijia; Zhang, Ya; Vierheilig, Julia, 0000-0002-9764-7534; Wells,
George F.; Yang, Yunfeng, 0000-0001-8274-6196; Deng, Ye,
0000-0002-7584-0632; Tu, Qichao; Wang, Aijie; Zhang, Tong; He, Zhili;
Keller, Jurg; Nielsen, Per H., 0000-0002-6402-1877; Alvarez, Pedro J.
J.; Criddle, Craig S.; Wagner, Michael, 0000-0002-9778-7684; Tiedje,
James M.; He, Qiang, 0000-0002-7155-6474; Curtis, Thomas P.; Stahl,
David A.; Alvarez-Cohen, Lisa; Rittmann, Bruce E.; Wen, Xianghua,
0000-0002-9792-8678; Zhou, Jizhong, 0000-0003-2014-0564 |
Nature Microbiology |
2019 |
| 25212 |
10.1038/s41579-018-0136-7 |
An Evolving View Of Methane Metabolism In The
Archaea |
Evans, Paul N.; Boyd, Joel A.; Leu, Andy O.; Woodcroft,
Ben J.; Parks, Donovan H., 0000-0001-6662-9010; Hugenholtz, Philip;
Tyson, Gene W., 0000-0001-8559-9427 |
Nature Reviews Microbiology |
2019 |
| 25221 |
10.1038/s41579-019-0191-8 |
The Ancestral And Industrialized Gut Microbiota And
Implications For Human Health |
Sonnenburg, Erica D.; Sonnenburg, Justin L.,
0000-0003-2299-6817 |
Nature Reviews Microbiology |
2019 |
| 25235 |
10.1038/s41579-019-0256-8 |
Diet<U+2013>Microbiota Interactions And
Personalized Nutrition |
Kolodziejczyk, Aleksandra A.; Zheng, Danping; Elinav,
Eran, 0000-0002-5775-2110 |
Nature Reviews Microbiology |
2019 |
| 25571 |
10.1038/s41586-018-0617-x |
Temporal Development Of The Gut Microbiome In Early
Childhood From The Teddy Study |
Stewart, Christopher J.; Ajami, Nadim J.; O’Brien,
Jacqueline L.; Hutchinson, Diane S.; Smith, Daniel P.; Wong, Matthew C.;
Ross, Matthew C.; Lloyd, Richard E.; Doddapaneni, Harshavardhan;
Metcalf, Ginger A.; Muzny, Donna; Gibbs, Richard A.; Vatanen, Tommi;
Huttenhower, Curtis; Xavier, Ramnik J.; Rewers, Marian; Hagopian,
William; Toppari, Jorma; Ziegler, Anette-G.; She, Jin-Xiong; Akolkar,
Beena; Lernmark, Ake; Hyoty, Heikki; Vehik, Kendra; Krischer, Jeffrey
P.; Petrosino, Joseph F. |
Nature |
2018 |
| 25573 |
10.1038/s41586-018-0620-2 |
The Human Gut Microbiome In Early-Onset Type 1 Diabetes
From The Teddy Study |
Vatanen, Tommi; Franzosa, Eric A.; Schwager, Randall;
Tripathi, Surya; Arthur, Timothy D.; Vehik, Kendra; Lernmark, Ake;
Hagopian, William A.; Rewers, Marian J.; She, Jin-Xiong; Toppari, Jorma;
Ziegler, Anette-G.; Akolkar, Beena; Krischer, Jeffrey P.; Stewart,
Christopher J.; Ajami, Nadim J.; Petrosino, Joseph F.; Gevers, Dirk;
Lahdesmaki, Harri; Vlamakis, Hera; Huttenhower, Curtis; Xavier, Ramnik
J. |
Nature |
2018 |
| 25680 |
10.1038/s41586-019-0965-1 |
A New Genomic Blueprint Of The Human Gut
Microbiota |
Almeida, Alexandre; Mitchell, Alex L.; Boland, Miguel;
Forster, Samuel C.; Gloor, Gregory B.; Tarkowska, Aleksandra; Lawley,
Trevor D.; Finn, Robert D. |
Nature |
2019 |
| 25722 |
10.1038/s41586-019-1058-x |
New Insights From Uncultivated Genomes Of The Global
Human Gut Microbiome |
Nayfach, Stephen; Shi, Zhou Jason; Seshadri, Rekha;
Pollard, Katherine S.; Kyrpides, Nikos C. |
Nature |
2019 |
| 25725 |
10.1038/s41586-019-1065-y |
Structural Variation In The Gut Microbiome Associates
With Host Health |
Zeevi, David; Korem, Tal; Godneva, Anastasia; Bar,
Noam; Kurilshikov, Alexander; Lotan-Pompan, Maya; Weinberger, Adina; Fu,
Jingyuan; Wijmenga, Cisca; Zhernakova, Alexandra; Segal, Eran |
Nature |
2019 |
| 25847 |
10.1038/s41586-019-1451-5 |
Human Placenta Has No Microbiome But Can Contain
Potential Pathogens |
De Goffau, Marcus C.; Lager, Susanne; Sovio, Ulla;
Gaccioli, Francesca; Cook, Emma; Peacock, Sharon J.; Parkhill, Julian;
Charnock-Jones, D. Stephen; Smith, Gordon C. S. |
Nature |
2019 |
| 25873 |
10.1038/s41586-019-1560-1 |
Stunted Microbiota And Opportunistic Pathogen
Colonization In Caesarean-Section Birth |
Shao, Yan; Forster, Samuel C.; Tsaliki, Evdokia;
Vervier, Kevin; Strang, Angela; Simpson, Nandi; Kumar, Nitin; Stares,
Mark D.; Rodger, Alison; Brocklehurst, Peter; Field, Nigel; Lawley,
Trevor D. |
Nature |
2019 |
| 25971 |
10.1038/s41586-019-1916-6 |
Isolation Of An Archaeon At The
Prokaryote<U+2013>Eukaryote Interface |
Imachi, Hiroyuki; Nobu, Masaru K.; Nakahara, Nozomi;
Morono, Yuki; Ogawara, Miyuki; Takaki, Yoshihiro; Takano, Yoshinori;
Uematsu, Katsuyuki; Ikuta, Tetsuro; Ito, Motoo; Matsui, Yohei; Miyazaki,
Masayuki; Murata, Kazuyoshi; Saito, Yumi; Sakai, Sanae; Song, Chihong;
Tasumi, Eiji; Yamanaka, Yuko; Yamaguchi, Takashi; Kamagata, Yoichi;
Tamaki, Hideyuki; Takai, Ken |
Nature |
2020 |
| 26179 |
10.1038/s41587-018-0008-8 |
1,520 Reference Genomes From Cultivated Human Gut
Bacteria Enable Functional Microbiome Analyses |
Zou, Yuanqiang, 0000-0003-2380-264X; Xue, Wenbin; Luo,
Guangwen; Deng, Ziqing, 0000-0001-8726-0160; Qin, Panpan,
0000-0002-7307-8736; Guo, Ruijin; Sun, Haipeng; Xia, Yan; Liang, Suisha;
Dai, Ying; Wan, Daiwei; Jiang, Rongrong; Su, Lili; Feng, Qiang; Jie,
Zhuye; Guo, Tongkun; Xia, Zhongkui; Liu, Chuan; Yu, Jinghong; Lin,
Yuxiang; Tang, Shanmei; Huo, Guicheng; Xu, Xun; Hou, Yong,
0000-0002-0420-0726; Liu, Xin, 0000-0003-3256-2940; Wang, Jian; Yang,
Huanming; Kristiansen, Karsten, 0000-0002-6024-0917; Li, Junhua,
0000-0001-6784-1873; Jia, Huijue, 0000-0002-3592-126X; Xiao, Liang,
0000-0003-0836-4397 |
Nature Biotechnology |
2019 |
| 26180 |
10.1038/s41587-018-0009-7 |
A Human Gut Bacterial Genome And Culture Collection For
Improved Metagenomic Analyses |
Forster, Samuel C., 0000-0003-4144-2537; Kumar, Nitin;
Anonye, Blessing O., 0000-0003-1619-5554; Almeida, Alexandre,
0000-0001-8803-0893; Viciani, Elisa; Stares, Mark D.; Dunn, Matthew;
Mkandawire, Tapoka T.; Zhu, Ana; Shao, Yan, 0000-0002-8662-0504; Pike,
Lindsay J.; Louie, Thomas; Browne, Hilary P., 0000-0002-1305-2470;
Mitchell, Alex L.; Neville, B. Anne; Finn, Robert D.,
0000-0001-8626-2148; Lawley, Trevor D. |
Nature Biotechnology |
2019 |
| 26220 |
10.1038/s41587-019-0191-2 |
Hybrid Metagenomic Assembly Enables High-Resolution
Analysis Of Resistance Determinants And Mobile Elements In Human
Microbiomes |
Bertrand, Denis; Shaw, Jim; Kalathiyappan, Manesh; Ng,
Amanda Hui Qi; Kumar, M. Senthil; Li, Chenhao, 0000-0003-1182-6804;
Dvornicic, Mirta; Soldo, Janja Paliska; Koh, Jia Yu; Tong, Chengxuan;
Ng, Oon Tek; Barkham, Timothy, 0000-0003-0975-2244; Young, Barnaby;
Marimuthu, Kalisvar; Chng, Kern Rei; Sikic, Mile, 0000-0002-8370-0891;
Nagarajan, Niranjan, 0000-0003-0850-5604 |
Nature Biotechnology |
2019 |
| 26225 |
10.1038/s41587-019-0202-3 |
Compendium Of 4,941 Rumen Metagenome-Assembled Genomes
For Rumen Microbiome Biology And Enzyme Discovery |
Stewart, Robert D.; Auffret, Marc D.,
0000-0002-2321-8219; Warr, Amanda; Walker, Alan W., 0000-0001-5099-8495;
Roehe, Rainer, 0000-0002-4880-3756; Watson, Mick,
0000-0003-4211-0358 |
Nature Biotechnology |
2019 |
| 26228 |
10.1038/s41587-019-0209-9 |
Reproducible, Interactive, Scalable And Extensible
Microbiome Data Science Using Qiime 2 |
Bolyen, Evan, 0000-0002-5362-6782; Rideout, Jai Ram,
0000-0003-2587-1454; Dillon, Matthew R., 0000-0002-7713-1952; Bokulich,
Nicholas A., 0000-0002-1784-8935; Abnet, Christian C.,
0000-0002-3008-7843; Al-Ghalith, Gabriel A., 0000-0002-6953-6319;
Alexander, Harriet; Alm, Eric J., 0000-0001-8294-9364; Arumugam,
Manimozhiyan, 0000-0002-0886-9101; Asnicar, Francesco,
0000-0003-3732-1468; Bai, Yang, 0000-0003-2652-7022; Bisanz, Jordan E.,
0000-0002-8649-1706; Bittinger, Kyle; Brejnrod, Asker; Brislawn, Colin
J.; Brown, C. Titus, 0000-0001-6001-2677; Callahan, Benjamin J.,
0000-0002-8752-117X; Caraballo-Rodriguez, Andres Mauricio,
0000-0001-5499-2728; Chase, John; Cope, Emily K.; Da Silva, Ricardo;
Diener, Christian, 0000-0002-7476-0868; Dorrestein, Pieter C.,
0000-0002-3003-1030; Douglas, Gavin M.; Durall, Daniel M.,
0000-0001-7414-4443; Duvallet, Claire, 0000-0002-8093-8394; Edwardson,
Christian F., 0000-0001-7524-7209; Ernst, Madeleine; Estaki, Mehrbod;
Fouquier, Jennifer, 0000-0002-0975-8235; Gauglitz, Julia M.; Gibbons,
Sean M., 0000-0002-8724-7916; Gibson, Deanna L.; Gonzalez, Antonio;
Gorlick, Kestrel; Guo, Jiarong; Hillmann, Benjamin; Holmes, Susan,
0000-0002-2208-8168; Holste, Hannes, 0000-0001-7739-6590; Huttenhower,
Curtis, 0000-0002-1110-0096; Huttley, Gavin A.; Janssen, Stefan,
0000-0003-0955-0589; Jarmusch, Alan K.; Jiang, Lingjing; Kaehler,
Benjamin D.; Kang, Kyo Bin, 0000-0003-3290-1017; Keefe, Christopher R.,
0000-0002-4289-0991; Keim, Paul; Kelley, Scott T.; Knights, Dan;
Koester, Irina; Kosciolek, Tomasz, 0000-0002-9915-7387; Kreps, Jorden,
0000-0003-3758-6458; Langille, Morgan G. I.; Lee, Joslynn; Ley, Ruth;
Liu, Yong-Xin, 0000-0003-1832-9835; Loftfield, Erikka,
0000-0002-3573-8748; Lozupone, Catherine, 0000-0003-4786-7202; Maher,
Massoud; Marotz, Clarisse, 0000-0002-1520-8854; Martin, Bryan D.,
0000-0002-8002-5296; Mcdonald, Daniel, 0000-0003-0876-9060; Mciver,
Lauren J.; Melnik, Alexey V., 0000-0002-4645-8880; Metcalf, Jessica L.;
Morgan, Sydney C.; Morton, Jamie T.; Naimey, Ahmad Turan; Navas-Molina,
Jose A., 0000-0003-4595-920X; Nothias, Louis Felix; Orchanian, Stephanie
B., 0000-0002-2491-1074; Pearson, Talima, 0000-0003-3696-041X; Peoples,
Samuel L.; Petras, Daniel, 0000-0002-6561-3022; Preuss, Mary Lai;
Pruesse, Elmar; Rasmussen, Lasse Buur; Rivers, Adam,
0000-0002-3703-834X; Robeson, Michael S., 0000-0001-7119-6301;
Rosenthal, Patrick; Segata, Nicola, 0000-0002-1583-5794; Shaffer,
Michael; Shiffer, Arron; Sinha, Rashmi; Song, Se Jin,
0000-0003-0750-5709; Spear, John R.; Swafford, Austin D.; Thompson, Luke
R., 0000-0002-3911-1280; Torres, Pedro J.; Trinh, Pauline; Tripathi,
Anupriya; Turnbaugh, Peter J., 0000-0002-0888-2875; Ul-Hasan, Sabah; Van
Der Hooft, Justin J. J., 0000-0002-9340-5511; Vargas, Fernando;
Vazquez-Baeza, Yoshiki; Vogtmann, Emily, 0000-0003-1355-5593; Von
Hippel, Max, 0000-0003-0288-5802; Walters, William; Wan, Yunhu; Wang,
Mingxun; Warren, Jonathan, 0000-0003-3381-3852; Weber, Kyle C.;
Williamson, Charles H. D.; Willis, Amy D., 0000-0002-2802-4317; Xu,
Zhenjiang Zech; Zaneveld, Jesse R.; Zhang, Yilong; Zhu, Qiyun,
0000-0002-3568-6271; Knight, Rob, 0000-0002-0975-9019; Caporaso, J.
Gregory, 0000-0002-8865-1670 |
Nature Biotechnology |
2019 |
| 26265 |
10.1038/s41587-020-0422-6 |
Complete, Closed Bacterial Genomes From Microbiomes
Using Nanopore Sequencing |
Moss, Eli L.; Maghini, Dylan G.; Bhatt, Ami S.,
0000-0001-8099-2975 |
Nature Biotechnology |
2020 |
| 26281 |
10.1038/s41587-020-0501-8 |
A Complete Domain-To-Species Taxonomy For Bacteria And
Archaea |
Parks, Donovan H., 0000-0001-6662-9010; Chuvochina,
Maria; Chaumeil, Pierre-Alain; Rinke, Christian, 0000-0003-4632-1187;
Mussig, Aaron J., 0000-0002-9988-0866; Hugenholtz, Philip,
0000-0001-5386-7925 |
Nature Biotechnology |
2020 |
| 26288 |
10.1038/s41587-020-0548-6 |
Picrust2 For Prediction Of Metagenome Functions |
Douglas, Gavin M.; Maffei, Vincent J.,
0000-0002-5339-5945; Zaneveld, Jesse R.; Yurgel, Svetlana N.; Brown,
James R., 0000-0002-9368-627X; Taylor, Christopher M.,
0000-0002-7983-5275; Huttenhower, Curtis, 0000-0002-1110-0096; Langille,
Morgan G. I., 0000-0002-6604-3009 |
Nature Biotechnology |
2020 |
| 26293 |
10.1038/s41587-020-0603-3 |
A Unified Catalog Of 204,938 Reference Genomes From The
Human Gut Microbiome |
Almeida, Alexandre, 0000-0001-8803-0893; Nayfach,
Stephen; Boland, Miguel; Strozzi, Francesco, 0000-0002-6845-6982;
Beracochea, Martin, 0000-0003-3472-3736; Shi, Zhou Jason; Pollard,
Katherine S., 0000-0002-9870-6196; Sakharova, Ekaterina; Parks, Donovan
H., 0000-0001-6662-9010; Hugenholtz, Philip, 0000-0001-5386-7925;
Segata, Nicola, 0000-0002-1583-5794; Kyrpides, Nikos C.,
0000-0002-6131-0462; Finn, Robert D., 0000-0001-8626-2148 |
Nature Biotechnology |
2020 |
| 26300 |
10.1038/s41587-020-0718-6 |
A Genomic Catalog Of Earth’S Microbiomes |
Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary,
Daniel, 0000-0002-3491-0198; Varghese, Neha; Schulz, Frederik,
0000-0002-4932-4677; Wu, Dongying; Paez-Espino, David,
0000-0002-2939-5398; Chen, I-Min, 0000-0003-2026-9798; Huntemann,
Marcel, 0000-0002-1284-3748; Palaniappan, Krishna; Ladau, Joshua;
Mukherjee, Supratim, 0000-0002-6322-2271; Reddy, T. B. K.,
0000-0002-0871-5567; Nielsen, Torben; Kirton, Edward; Faria, Jose P.;
Edirisinghe, Janaka N.; Henry, Christopher S.; Jungbluth, Sean P.;
Chivian, Dylan, 0000-0001-8189-8729; Dehal, Paramvir; Wood-Charlson,
Elisha M., 0000-0001-9557-7715; Arkin, Adam P.; Tringe, Susannah G.,
0000-0001-6479-8427; Visel, Axel, 0000-0002-4130-7784; Abreu, Helena;
Acinas, Silvia G.; Allen, Eric; Allen, Michelle A.; Alteio, Lauren V.;
Andersen, Gary; Anesio, Alexandre M.; Attwood, Graeme; Avila-Magana,
Viridiana; Badis, Yacine; Bailey, Jake; Baker, Brett; Baldrian, Petr;
Barton, Hazel A.; Beck, David A. C.; Becraft, Eric D.; Beller, Harry R.;
Beman, J. Michael; Bernier-Latmani, Rizlan; Berry, Timothy D.;
Bertagnolli, Anthony; Bertilsson, Stefan; Bhatnagar, Jennifer M.; Bird,
Jordan T.; Blanchard, Jeffrey L.; Blumer-Schuette, Sara E.; Bohannan,
Brendan; Borton, Mikayla A.; Brady, Allyson; Brawley, Susan H.; Brodie,
Juliet; Brown, Steven; Brum, Jennifer R.; Brune, Andreas; Bryant, Donald
A.; Buchan, Alison; Buckley, Daniel H.; Buongiorno, Joy; Cadillo-Quiroz,
Hinsby; Caffrey, Sean M.; Campbell, Ashley N.; Campbell, Barbara; Carr,
Stephanie; Carroll, Jolynn; Cary, S. Craig; Cates, Anna M.; Cattolico,
Rose Ann; Cavicchioli, Ricardo; Chistoserdova, Ludmila; Coleman, Maureen
L.; Constant, Philippe; Conway, Jonathan M.; Mac Cormack, Walter P.;
Crowe, Sean; Crump, Byron; Currie, Cameron; Daly, Rebecca; Deangelis,
Kristen M.; Denef, Vincent; Denman, Stuart E.; Desta, Adey; Dionisi,
Hebe; Dodsworth, Jeremy; Dombrowski, Nina; Donohue, Timothy; Dopson,
Mark; Driscoll, Timothy; Dunfield, Peter; Dupont, Christopher L.;
Dynarski, Katherine A.; Edgcomb, Virginia; Edwards, Elizabeth A.;
Elshahed, Mostafa S.; Figueroa, Israel; Flood, Beverly; Fortney,
Nathaniel; Fortunato, Caroline S.; Francis, Christopher; Gachon, Claire
M. M.; Garcia, Sarahi L.; Gazitua, Maria C.; Gentry, Terry; Gerwick,
Lena; Gharechahi, Javad; Girguis, Peter; Gladden, John; Gradoville,
Mary; Grasby, Stephen E.; Gravuer, Kelly; Grettenberger, Christen L.;
Gruninger, Robert J.; Guo, Jiarong; Habteselassie, Mussie Y.; Hallam,
Steven J.; Hatzenpichler, Roland; Hausmann, Bela; Hazen, Terry C.;
Hedlund, Brian; Henny, Cynthia; Herfort, Lydie; Hernandez, Maria;
Hershey, Olivia S.; Hess, Matthias; Hollister, Emily B.; Hug, Laura A.;
Hunt, Dana; Jansson, Janet; Jarett, Jessica; Kadnikov, Vitaly V.; Kelly,
Charlene; Kelly, Robert; Kelly, William; Kerfeld, Cheryl A.; Kimbrel,
Jeff; Klassen, Jonathan L.; Konstantinidis, Konstantinos T.; Lee, Laura
L.; Li, Wen-Jun; Loder, Andrew J.; Loy, Alexander; Lozada, Mariana;
Macgregor, Barbara; Magnabosco, Cara; Maria Da Silva, Aline; Mckay, R.
Michael; Mcmahon, Katherine; Mcsweeney, Chris S.; Medina, Monica;
Meredith, Laura; Mizzi, Jessica; Mock, Thomas; Momper, Lily; Moran, Mary
Ann; Morgan-Lang, Connor; Moser, Duane; Muyzer, Gerard; Myrold, David;
Nash, Maisie; Nesbo, Camilla L.; Neumann, Anthony P.; Neumann, Rebecca
B.; Noguera, Daniel; Northen, Trent; Norton, Jeanette; Nowinski, Brent;
Nusslein, Klaus; O’Malley, Michelle A.; Oliveira, Rafael S.; Maia De
Oliveira, Valeria; Onstott, Tullis; Osvatic, Jay; Ouyang, Yang;
Pachiadaki, Maria; Parnell, Jacob; Partida-Martinez, Laila P.; Peay,
Kabir G.; Pelletier, Dale; Peng, Xuefeng; Pester, Michael; Pett-Ridge,
Jennifer; Peura, Sari; Pjevac, Petra; Plominsky, Alvaro M.; Poehlein,
Anja; Pope, Phillip B.; Ravin, Nikolai; Redmond, Molly C.; Reiss,
Rebecca; Rich, Virginia; Rinke, Christian; Rodrigues, Jorge L. Mazza;
Rodriguez-Reillo, William; Rossmassler, Karen; Sackett, Joshua;
Salekdeh, Ghasem Hosseini; Saleska, Scott; Scarborough, Matthew;
Schachtman, Daniel; Schadt, Christopher W.; Schrenk, Matthew; Sczyrba,
Alexander; Sengupta, Aditi; Setubal, Joao C.; Shade, Ashley; Sharp,
Christine; Sherman, David H.; Shubenkova, Olga V.; Sierra-Garcia, Isabel
Natalia; Simister, Rachel; Simon, Holly; Sjoling, Sara; Slonczewski,
Joan; Correa De Souza, Rafael Soares; Spear, John R.; Stegen, James C.;
Stepanauskas, Ramunas; Stewart, Frank; Suen, Garret; Sullivan, Matthew;
Sumner, Dawn; Swan, Brandon K.; Swingley, Wesley; Tarn, Jonathan;
Taylor, Gordon T.; Teeling, Hanno; Tekere, Memory; Teske, Andreas;
Thomas, Torsten; Thrash, Cameron; Tiedje, James; Ting, Claire S.; Tully,
Benjamin; Tyson, Gene; Ulloa, Osvlado; Valentine, David L.; Van Goethem,
Marc W.; Vandergheynst, Jean; Verbeke, Tobin J.; Vollmers, John;
Vuillemin, Aurele; Waldo, Nicholas B.; Walsh, David A.; Weimer, Bart C.;
Whitman, Thea; Van Der Wielen, Paul; Wilkins, Michael; Williams, Timothy
J.; Woodcroft, Ben; Woolet, Jamie; Wrighton, Kelly; Ye, Jun; Young,
Erica B.; Youssef, Noha H.; Yu, Feiqiao Brian; Zemskaya, Tamara I.;
Ziels, Ryan; Woyke, Tanja, 0000-0002-9485-5637; Mouncey, Nigel J.,
0000-0001-5380-1256; Ivanova, Natalia N., 0000-0002-5802-9485; Kyrpides,
Nikos C., 0000-0002-6131-0462; Eloe-Fadrosh, Emiley A.,
0000-0002-8162-1276 |
Nature Biotechnology |
2020 |
| 26564 |
10.1038/s41591-018-0160-1 |
Depicting The Composition Of Gut Microbiota In A
Population With Varied Ethnic Origins But Shared Geography |
Deschasaux, Melanie, 0000-0002-3359-420X; Bouter,
Kristien E.; Prodan, Andrei; Levin, Evgeni; Groen, Albert K.; Herrema,
Hilde; Tremaroli, Valentina; Bakker, Guido J.; Attaye, Ilias;
Pinto-Sietsma, Sara-Joan; Van Raalte, Daniel H.; Snijder, Marieke B.;
Nicolaou, Mary; Peters, Ron; Zwinderman, Aeilko H.; Backhed, Fredrik;
Nieuwdorp, Max |
Nature Medicine |
2018 |
| 26565 |
10.1038/s41591-018-0164-x |
Regional Variation Limits Applications Of Healthy Gut
Microbiome Reference Ranges And Disease Models |
He, Yan; Wu, Wei; Zheng, Hui-Min; Li, Pan; Mcdonald,
Daniel; Sheng, Hua-Fang; Chen, Mu-Xuan; Chen, Zi-Hui; Ji, Gui-Yuan;
Zheng, Zhong-Dai-Xi; Mujagond, Prabhakar; Chen, Xiao-Jiao; Rong, Zu-Hua;
Chen, Peng; Lyu, Li-Yi; Wang, Xian; Wu, Chong-Bin; Yu, Nan; Xu, Yan-Jun;
Yin, Jia; Raes, Jeroen; Knight, Rob, 0000-0002-0975-9019; Ma, Wen-Jun;
Zhou, Hong-Wei, 0000-0003-2472-8541 |
Nature Medicine |
2018 |
| 26683 |
10.1038/s41591-019-0559-3 |
A Library Of Human Gut Bacterial Isolates Paired With
Longitudinal Multiomics Data Enables Mechanistic Microbiome
Research |
Poyet, M.; Groussin, M.; Gibbons, S. M.,
0000-0002-8724-7916; Avila-Pacheco, J.; Jiang, X.; Kearney, S. M.;
Perrotta, A. R.; Berdy, B., 0000-0002-8593-0762; Zhao, S.; Lieberman, T.
D.; Swanson, P. K.; Smith, M.; Roesemann, S., 0000-0002-9466-0733;
Alexander, J. E.; Rich, S. A.; Livny, J.; Vlamakis, H.; Clish, C.,
0000-0001-8259-9245; Bullock, K.; Deik, A.; Scott, J.; Pierce, K. A.;
Xavier, R. J.; Alm, E. J., 0000-0001-8294-9364 |
Nature Medicine |
2019 |
| 26721 |
10.1038/s41591-020-0761-3 |
Viable Bacterial Colonization Is Highly Limited In The
Human Intestine In Utero |
Rackaityte, E., 0000-0003-3889-8082; Halkias, J.,
0000-0003-0721-8961; Fukui, E. M.; Mendoza, V. F.; Hayzelden, C.;
Crawford, E. D., 0000-0003-4182-2337; Fujimura, K. E.; Burt, T. D.,
0000-0001-7933-529X; Lynch, S. V., 0000-0001-5695-7336 |
Nature Medicine |
2020 |
| 26824 |
10.1038/s41592-018-0141-9 |
Qiita: Rapid, Web-Enabled Microbiome Meta-Analysis |
Gonzalez, Antonio; Navas-Molina, Jose A.,
0000-0003-4595-920X; Kosciolek, Tomasz; Mcdonald, Daniel; Vazquez-Baeza,
Yoshiki; Ackermann, Gail; Dereus, Jeff; Janssen, Stefan; Swafford,
Austin D.; Orchanian, Stephanie B.; Sanders, Jon G.; Shorenstein,
Joshua; Holste, Hannes, 0000-0001-7739-6590; Petrus, Semar;
Robbins-Pianka, Adam; Brislawn, Colin J.; Wang, Mingxun; Rideout, Jai
Ram, 0000-0003-2587-1454; Bolyen, Evan; Dillon, Matthew; Caporaso, J.
Gregory, 0000-0002-8865-1670; Dorrestein, Pieter C.,
0000-0002-3003-1030; Knight, Rob, 0000-0002-0975-9019 |
Nature Methods |
2018 |
| 30612 |
10.1093/bioinformatics/btz848 |
Gtdb-Tk: A Toolkit To Classify Genomes With The Genome
Taxonomy Database |
Chaumeil, Pierre-Alain; Mussig, Aaron J; Hugenholtz,
Philip; Parks, Donovan H |
Bioinformatics |
2019 |
| 30613 |
10.1093/bioinformatics/btz859 |
Kofamkoala: Kegg Ortholog Assignment Based On Profile
Hmm And Adaptive Score Threshold |
Aramaki, Takuya; Blanc-Mathieu, Romain; Endo, Hisashi;
Ohkubo, Koichi; Kanehisa, Minoru; Goto, Susumu; Ogata, Hiroyuki |
Bioinformatics |
2019 |
| 30874 |
10.1093/femsec/fiz045 |
Issues And Current Standards Of Controls In Microbiome
Research |
Hornung, Bastian V H; Zwittink, Romy D; Kuijper, Ed
J |
Fems Microbiology Ecology |
2019 |
| 30902 |
10.1093/gigascience/giz043 |
Ultra-Deep, Long-Read Nanopore Sequencing Of Mock
Microbial Community Standards |
Nicholls, Samuel M, 0000-0003-4081-065X; Quick, Joshua
C, 0000-0001-6376-871X; Tang, Shuiquan; Loman, Nicholas J,
0000-0002-9843-8988 |
Gigascience |
2019 |
| 31237 |
10.1093/nar/gkz246 |
Annotree: Visualization And Exploration Of A
Functionally Annotated Microbial Tree Of Life |
Mendler, Kerrin; Chen, Han; Parks, Donovan H; Lobb,
Briallen; Hug, Laura A; Doxey, Andrew C |
Nucleic Acids Research |
2019 |
| 31376 |
10.1093/sysbio/syy054 |
Epa-Ng: Massively Parallel Evolutionary Placement Of
Genetic Sequences |
Barbera, Pierre; Kozlov, Alexey M; Czech, Lucas; Morel,
Benoit; Darriba, Diego; Flouri, Toma<U+0161>; Stamatakis,
Alexandros |
Systematic Biology |
2018 |
| 31652 |
10.1101/gr.258640.119 |
Accurate And Complete Genomes From Metagenomes |
Chen, Lin-Xing, 0000-0003-2774-1952; Anantharaman,
Karthik, 0000-0002-9584-2491; Shaiber, Alon, 0000-0002-4806-9280; Eren,
A. Murat, 0000-0001-9013-4827; Banfield, Jillian F.,
0000-0001-8203-8771 |
Genome Research |
2020 |
| 32734 |
10.1111/1755-0998.13011 |
Laboratory Contamination Over Time During Low‐Biomass
Sample Analysis |
Weyrich, Laura S., 0000-0001-5243-4634; Farrer, Andrew
G.; Eisenhofer, Raphael; Arriola, Luis A.; Young, Jennifer; Selway,
Caitlin A.; Handsley‐Davis, Matilda; Adler, Christina J.; Breen, James;
Cooper, Alan |
Molecular Ecology Resources |
2019 |
| 33474 |
10.1126/sciadv.aau9124 |
Antibiotic Resistance In European Wastewater Treatment
Plants Mirrors The Pattern Of Clinical Antibiotic Resistance
Prevalence |
Parnanen, Katariina M. M., 0000-0003-2220-1738;
Narciso-Da-Rocha, Carlos, 0000-0001-6398-1633; Kneis, David,
0000-0002-6048-6984; Berendonk, Thomas U., 0000-0002-9301-1803; Cacace,
Damiano, 0000-0003-1725-1044; Do, Thi Thuy; Elpers, Christian;
Fatta-Kassinos, Despo; Henriques, Isabel; Jaeger, Thomas; Karkman,
Antti, 0000-0003-0983-3319; Martinez, Jose Luis; Michael, Stella G.;
Michael-Kordatou, Irene; O’Sullivan, Kristin; Rodriguez-Mozaz, Sara,
0000-0003-2962-8144; Schwartz, Thomas; Sheng, Hongjie; Sorum, Henning,
0000-0002-2834-3342; Stedtfeld, Robert D., 0000-0003-2678-7801; Tiedje,
James M., 0000-0002-8992-6218; Giustina, Saulo Varela Della; Walsh,
Fiona; Vaz-Moreira, Ivone; Virta, Marko, 0000-0001-5981-7566; Manaia,
Celia M., 0000-0002-3674-1789 |
Science Advances |
2019 |
| 34153 |
10.1128/cmr.00088-17 |
Mobile Genetic Elements Associated With Antimicrobial
Resistance |
Partridge, Sally R.; Kwong, Stephen M.; Firth, Neville;
Jensen, Slade O. |
Clinical Microbiology Reviews |
2018 |
| 34242 |
10.1128/msystems.00016-19 |
A Novel Sparse Compositional Technique Reveals
Microbial Perturbations |
Martino, Cameron; Morton, James T.; Marotz, Clarisse
A.; Thompson, Luke R., 0000-0002-3911-1280; Tripathi, Anupriya; Knight,
Rob; Zengler, Karsten |
Msystems |
2019 |
| 34243 |
10.1128/msystems.00031-18 |
American Gut: An Open Platform For Citizen Science
Microbiome Research |
Mcdonald, Daniel, 0000-0003-0876-9060; Hyde, Embriette;
Debelius, Justine W.; Morton, James T.; Gonzalez, Antonio; Ackermann,
Gail; Aksenov, Alexander A.; Behsaz, Bahar; Brennan, Caitriona; Chen,
Yingfeng; Deright Goldasich, Lindsay; Dorrestein, Pieter C.; Dunn,
Robert R.; Fahimipour, Ashkaan K.; Gaffney, James; Gilbert, Jack A.;
Gogul, Grant; Green, Jessica L.; Hugenholtz, Philip; Humphrey, Greg;
Huttenhower, Curtis; Jackson, Matthew A.; Janssen, Stefan,
0000-0003-0955-0589; Jeste, Dilip V.; Jiang, Lingjing; Kelley, Scott T.,
0000-0001-9547-4169; Knights, Dan; Kosciolek, Tomasz; Ladau, Joshua;
Leach, Jeff; Marotz, Clarisse; Meleshko, Dmitry; Melnik, Alexey V.;
Metcalf, Jessica L.; Mohimani, Hosein; Montassier, Emmanuel,
0000-0002-2313-1172; Navas-Molina, Jose; Nguyen, Tanya T.; Peddada,
Shyamal; Pevzner, Pavel; Pollard, Katherine S.; Rahnavard, Gholamali,
0000-0002-9710-0248; Robbins-Pianka, Adam; Sangwan, Naseer; Shorenstein,
Joshua; Smarr, Larry; Song, Se Jin, 0000-0003-0750-5709; Spector,
Timothy; Swafford, Austin D.; Thackray, Varykina G.; Thompson, Luke R.;
Tripathi, Anupriya; Vazquez-Baeza, Yoshiki; Vrbanac, Alison; Wischmeyer,
Paul; Wolfe, Elaine; Zhu, Qiyun; Knight, Rob |
Msystems |
2018 |
| 34245 |
10.1128/msystems.00069-18 |
Evaluating The Information Content Of Shallow Shotgun
Metagenomics |
Hillmann, Benjamin; Al-Ghalith, Gabriel A.,
0000-0002-6953-6319; Shields-Cutler, Robin R.; Zhu, Qiyun; Gohl, Daryl
M.; Beckman, Kenneth B.; Knight, Rob; Knights, Dan |
Msystems |
2018 |
| 34247 |
10.1128/msystems.00186-19 |
Quantifying And Understanding Well-To-Well
Contamination In Microbiome Research |
Minich, Jeremiah J.; Sanders, Jon G.; Amir, Amnon;
Humphrey, Greg; Gilbert, Jack A.; Knight, Rob |
Msystems |
2019 |
| 34254 |
10.1128/msystems.00290-19 |
Controlling For Contaminants In Low-Biomass 16S Rrna
Gene Sequencing Experiments |
Karstens, Lisa; Asquith, Mark; Davin, Sean; Fair,
Damien; Gregory, W. Thomas; Wolfe, Alan J.; Braun, Jonathan; Mcweeney,
Shannon |
Msystems |
2019 |
| 34266 |
10.1136/annrheumdis-2018-214514 |
Prevotella Copri In Individuals At Risk For Rheumatoid
Arthritis |
Alpizar-Rodriguez, Deshire, 0000-0002-6930-0517;
Lesker, Till Robin; Gronow, Achim; Gilbert, Benoit; Raemy, Elena;
Lamacchia, Celine; Gabay, Cem; Finckh, Axel; Strowig, Till |
Annals Of The Rheumatic Diseases |
2019 |
| 34481 |
10.1136/gutjnl-2019-319654 |
Mediterranean Diet Intervention Alters The Gut
Microbiome In Older People Reducing Frailty And Improving Health Status:
The Nu-Age 1-Year Dietary Intervention Across Five European
Countries |
Ghosh, Tarini Shankar; Rampelli, Simone; Jeffery, Ian
B; Santoro, Aurelia; Neto, Marta; Capri, Miriam; Giampieri, Enrico;
Jennings, Amy, 0000-0001-5333-714X; Candela, Marco; Turroni, Silvia;
Zoetendal, Erwin G; Hermes, Gerben D A, 0000-0003-4314-9553; Elodie,
Caumon; Meunier, Nathalie; Brugere, Corinne Malpuech; Pujos-Guillot,
Estelle; Berendsen, Agnes M; De Groot, Lisette C P G M; Feskins, Edith J
M; Kaluza, Joanna, 0000-0001-9454-0929; Pietruszka, Barbara,
0000-0003-0731-8612; Bielak, Marta Jeruszka; Comte, Blandine;
Maijo-Ferre, Monica; Nicoletti, Claudio; De Vos, Willem M;
Fairweather-Tait, Susan; Cassidy, Aedin; Brigidi, Patrizia; Franceschi,
Claudio; O’Toole, Paul W, 0000-0001-5377-0824 |
Gut |
2020 |
| 34484 |
10.1136/gutjnl-2019-320438 |
Mediterranean Diet Intervention In Overweight And Obese
Subjects Lowers Plasma Cholesterol And Causes Changes In The Gut
Microbiome And Metabolome Independently Of Energy Intake |
Meslier, Victoria; Laiola, Manolo; Roager, Henrik
Munch, 0000-0002-2504-8313; De Filippis, Francesca; Roume, Hugo;
Quinquis, Benoit; Giacco, Rosalba; Mennella, Ilario; Ferracane, Rosalia;
Pons, Nicolas; Pasolli, Edoardo; Rivellese, Angela; Dragsted, Lars Ove,
0000-0003-0609-6317; Vitaglione, Paola; Ehrlich, Stanislav Dusko,
0000-0002-7563-4046; Ercolini, Danilo, 0000-0003-3061-9560 |
Gut |
2020 |
| 36501 |
10.1186/s40168-018-0470-z |
Optimizing Taxonomic Classification Of Marker-Gene
Amplicon Sequences With Qiime 2’S Q2-Feature-Classifier Plugin |
Bokulich, Nicholas A.; Kaehler, Benjamin D.; Rideout,
Jai Ram; Dillon, Matthew; Bolyen, Evan; Knight, Rob; Huttley, Gavin A.;
Gregory Caporaso, J. |
Microbiome |
2018 |
| 36502 |
10.1186/s40168-018-0541-1 |
Metawrap―A Flexible Pipeline For Genome-Resolved
Metagenomic Data Analysis |
Uritskiy, Gherman V.; Diruggiero, Jocelyne,
0000-0001-6721-8061; Taylor, James |
Microbiome |
2018 |
| 36503 |
10.1186/s40168-018-0575-4 |
Lack Of Detection Of A Human Placenta Microbiome In
Samples From Preterm And Term Deliveries |
Leiby, Jacob S.; Mccormick, Kevin; Sherrill-Mix, Scott;
Clarke, Erik L.; Kessler, Lyanna R.; Taylor, Louis J.; Hofstaedter,
Casey E.; Roche, Aoife M.; Mattei, Lisa M.; Bittinger, Kyle; Elovitz,
Michal A.; Leite, Rita; Parry, Samuel; Bushman, Frederic D.,
0000-0003-4740-4056 |
Microbiome |
2018 |
| 36506 |
10.1186/s40168-018-0605-2 |
Simple Statistical Identification And Removal Of
Contaminant Sequences In Marker-Gene And Metagenomics Data |
Davis, Nicole M.; Proctor, Diana M.; Holmes, Susan P.;
Relman, David A.; Callahan, Benjamin J., 0000-0002-8752-117X |
Microbiome |
2018 |
| 36512 |
10.1186/s40168-019-0663-0 |
Mobile Antibiotic Resistome In Wastewater Treatment
Plants Revealed By Nanopore Metagenomic Sequencing |
Che, You; Xia, Yu; Liu, Lei; Li, An-Dong; Yang, Yu;
Zhang, Tong, 0000-0003-1148-4322 |
Microbiome |
2019 |
| 37098 |
10.1371/journal.pbio.2006842 |
Gut Microbiota Diversity Across Ethnicities In The
United States |
Brooks, Andrew W., 0000-0002-9237-5349; Priya,
Sambhawa; Blekhman, Ran; Bordenstein, Seth R. |
Plos Biology |
2018 |
| 37103 |
10.1371/journal.pbio.3000102 |
Evolutionary Dynamics Of Bacteria In The Gut Microbiome
Within And Across Hosts |
Garud, Nandita R., 0000-0003-4217-4407; Good, Benjamin
H., 0000-0002-7757-3347; Hallatschek, Oskar, 0000-0002-1312-5975;
Pollard, Katherine S., 0000-0002-9870-6196 |
Plos Biology |
2019 |
| 38489 |
10.3389/fmicb.2019.01124 |
The Not-So-Sterile Womb: Evidence That The Human Fetus
Is Exposed To Bacteria Prior To Birth |
Stinson, Lisa F.; Boyce, Mary C.; Payne, Matthew S.;
Keelan, Jeffrey A. |
Frontiers In Microbiology |
2019 |
| 38575 |
10.3389/fnut.2019.00004 |
Breast Milk Microbiota Is Shaped By Mode Of Delivery
And Intrapartum Antibiotic Exposure |
Hermansson, Henriina; Kumar, Himanshu; Collado, Maria
Carmen; Salminen, Seppo; Isolauri, Erika; Rautava, Samuli |
Frontiers In Nutrition |
2019 |
| 38579 |
10.3389/fnut.2019.00045 |
What’S Normal? Microbiomes In Human Milk And Infant
Feces Are Related To Each Other But Vary Geographically: The Inspire
Study |
Lackey, Kimberly A.; Williams, Janet E.; Meehan,
Courtney L.; Zachek, Jessica A.; Benda, Elizabeth D.; Price, William J.;
Foster, James A.; Sellen, Daniel W.; Kamau-Mbuthia, Elizabeth W.;
Kamundia, Egidioh W.; Mbugua, Samwel; Moore, Sophie E.; Prentice, Andrew
M.; K., Debela Gindola; Kvist, Linda J.; Otoo, Gloria E.; Garcia-Carral,
Cristina; Jimenez, Esther; Ruiz, Lorena; Rodriguez, Juan M.; Pareja,
Rossina G.; Bode, Lars; Mcguire, Mark A.; Mcguire, Michelle K. |
Frontiers In Nutrition |
2019 |
| 39640 |
10.3390/nu11122862 |
Effect Of Diet On The Gut Microbiota: Rethinking
Intervention Duration |
Leeming, Emily R; Johnson, Abigail J,
0000-0002-5998-4724; Spector, Tim D; Le Roy, Caroline I,
0000-0002-0341-751X |
Nutrients |
2019 |
| 39651 |
10.3390/nu12041039 |
Breast Milk, A Source Of Beneficial Microbes And
Associated Benefits For Infant Health |
Lyons, Katriona E.; Ryan, C. Anthony; Dempsey, Eugene
M.; Ross, R. Paul; Stanton, Catherine |
Nutrients |
2020 |
| 40673 |
10.7717/peerj.7359 |
Metabat 2: An Adaptive Binning Algorithm For Robust And
Efficient Genome Reconstruction From Metagenome Assemblies |
Kang, Dongwan D.; Li, Feng; Kirton, Edward,
0000-0003-1974-1768; Thomas, Ashleigh, 0000-0001-7422-5649; Egan, Rob,
0000-0001-7080-7801; An, Hong; Wang, Zhong, 0000-0002-6307-0458 |
Peerj |
2019 |